GMASS: a novel measure for genome assembly structural similarity

BMC Bioinformatics

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[1] 0000 0004 0532 8339, grid.258676.8, Department of Biomedical Science and Engineering, Konkuk University, 05029, Seoul, South Korea;

关键词: Measure;    Genome;    Assembly;    Structural similarity;   

DOI  :  10.1186/s12859-019-2710-z

来源: publisher

【 摘 要 】

BackgroundThanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have been developed to generate high quality de novo assemblies using the NGS reads, but their output is very different because of algorithmic differences. However, there are not properly structured measures to show the similarity or difference in assemblies.ResultsWe developed a new measure, called the GMASS score, for comparing two genome assemblies in terms of their structure. The GMASS score was developed based on the distribution pattern of the number and coverage of similar regions between a pair of assemblies. The new measure was able to show structural similarity between assemblies when evaluated by simulated assembly datasets. The application of the GMASS score to compare assemblies in recently published benchmark datasets showed the divergent performance of current assemblers as well as its ability to compare assemblies.ConclusionThe GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

【 授权许可】

CC BY